The Navy will spend $210 million to overhaul the $4.5 billion warship, which was commissioned in 2003 and arrived in its first home port, San Diego, in 2004.

The Reagan has completed five deployments in the past six years, returning from the most recent one in September.

Burke called the maintenance a “deep dive” into the parts of the ship that are unreachable when in the water. The list: propeller, shafts and fuel and water tanks.

“It’s a complete overhaul of your car, in a lot of ways,” Burke said. “A lot of body work, but also just a lot of deeper stuff. Going into those tanks that have been holding jet fuel or potable water for eight years now, making sure they are properly sealed and preserved.”

Civilian contractors at Puget Sound Naval Shipyard in Bremerton, Wash., will do the technical pieces. But the 2,500 sailors heading north with the ship will also work.

Burke said he plans to have his sailors strip and repaint the “island,” the iconic central tower that houses the ship’s bridge.

The systems that run the ship – radar and nuclear power, for example – will be upgraded. “It’s like putting more RAM into your computer,” said Senior Chief Petty Officer Dean Lohmeyer, the Reagan’s assistant public affairs officer.

The Navy has not officially said that the Reagan will return to North Island, which has room for three aircraft carriers. At one point in mid 2010, the Reagan, the Nimitz and the Carl Vinson were all parked at their home dock at the same time.

Since then, the Nimitz left for an overhaul period and was permanently reassigned to the Puget Sound region.

With the Reagan departing, the Carl Vinson – which left on a regular six-month deployment in November – is the only aircraft carrier assigned to San Diego Bay.

Doing “the math,” on Navy flattop assignments, Burke said he believes the Reagan is destined to return here.

Of the nation’s 11 aircraft carriers, the Pentagon wants to have them fairly split between the coasts, with an additional one in Japan. Washington state is the only other West Coast location for carriers.

Defense officials have hinted that a third carrier will call San Diego home by 2015 or 2016.

Burke said he doesn’t know when the Navy will announce where the Reagan will go after the overhaul. But, he said, “I expect it will be fairly soon.”

The skipper said the enormous upkeep required for these warships is another reason that the United States needs nearly a dozen.

“We know that we’re going to have to do these deep dives on ships on an eight to 10-year period” basis, Burke said.

“In order to have three out there all the time, three on ready standby, to go on a moment’s notice, you’ve got to have three or four more to be able to do this deep maintenance.”

The ship departed without fanfare on a warm, sunny San Diego winter day. Weather forecast for Bremerton: Rain tonight. Tomorrow cloudy, high of 45 degrees.